Chap 1 – Microbiology – Flashcards
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| Cell |
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| Fundamental unit of life |
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| Chemolithotropy |
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| A from of metabolism in which energy is generated from inorganic compounds |
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| Communication |
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| Interactions between cells using chemical signals |
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| Differentiation |
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| Modification of cellular components to form a new structure, such as a spore |
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| Ecosystem |
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| Organisms plus their nonliving environment |
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| Enrichment culture technique |
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| A method for isolating specific microorganisms from nature using specific culture media and incubation conditions |
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| Enzyme |
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| A protein or RNA catalyst that functions to speed up a chemical reaction |
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| Evolution |
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| Decent with modification leading to new forms or species |
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| Genome |
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| An organism's full complement of genes |
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| Genomics |
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| The identification and analysis of genomes |
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| Growth |
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| In microbiology, an increase in cell number with time |
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| Habitat |
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| The environment in which a microbial population resides |
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| Koch's postulates |
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| A set of criteria for proving that a given microorganism causes a certain disease |
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| Metabolism |
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| All biochemical reactions in a cell |
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| Microbial community |
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| Two or more populations of cells that coexist and interact in a habitat |
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| Microbial ecology |
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| The study of microorganisms in their natural environment |
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| Microorganism |
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| A microscopic organism consisting of a single cell or cell cluster or a virus |
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| Motility |
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| The movement of cell by some form of self propulsion |
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| Pathogen |
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| A disease causing microorganism |
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| Pure culture |
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| A culture containing a single kind of microorganism |
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| Spontaneous generation |
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| The hypothesis that living organisms can originate from nonliving matter |
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| Sterile |
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| Free of all living organisms cells and viruses |
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| Archaea |
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| One or two known domains of prokaryotes, compare with bacteria |
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| Autotroph |
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| An organism able to grow with carbon dioxide as it's sole carbon source |
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| Bacteria |
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| One of two known domains of prokaryotes, compare with Archaea |
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| Cell wall |
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| A rigid layer present outside the cytoplasmic membrane, confers structural strength to the cell and protection from osmotic layers |
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| Cell wall |
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| A rigid layer present outside the cytoplasmic membrane, confers structural strength to the cell and protection from osmotic layers |
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| Chemolithotroph |
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| An organism that obtains it's energy from the oxidation of inorganic compounds |
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| Chemoorganotroph |
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| an organism that obtains its energy from the oxidation of organic compounds |
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| chromosome |
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| a genetic element containing genes essential to cell function |
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| cyanobacteria |
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| Prokaryotic oxygenic phototrophs |
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| Cytoplasm |
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| the aqueous internal portion of a cell, bounded by the cytoplasmic membrane |
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| Cytoplasmic membrane |
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| the cell's permeability barrier to the environment; encloses the cytoplasm |
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| Domain |
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| The highest level of biological classification |
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| Endosymbiosis |
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| the theory that mitochondria and chloroplasts originated from Bacteria |
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| Eukarya |
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| The domain of life that includes all eukaryotic cells |
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| Eukaryote |
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| A cell having a membrane-enclosed nucleus and usually other membrane-enclosed organelles |
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| Evolution |
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| change in a line of descent over time leading to new species or varieties within a species |
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| Extremophile |
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| An organism that grows optimally under one or more environmental extremes |
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| Gram Stain |
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| A differential staining technique in which bacterial cells stain either pink (-) or purple (+) depending upon their structural makeup |
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| Heterotroph |
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| an organism that requires organic carbon as its carbon source |
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| Nucleoid |
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| the aggregated mass of DNA that constitutes the chromosome of cells of Bacteria and Archaea |
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| Nucleus |
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| a membrane-enclosed structure that contains the chromosomes in eukaryotic cells |
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| Organelle |
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| A membrane- enclosed structure, such as a mitochondrion or chloroplast, present in the cytoplasm of eukaryotic cells |
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| Phototroph |
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| an organism that obtains its energy from light |
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| phylogeny |
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| the evolutionary relationships between organisms |
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| plasmid |
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| an extrachromosomal genetic element nonessential for growth |
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| Prokaryote |
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| a cell that lacks a membrane-enclosed nucleus and other organelles |
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| Proteobacteria |
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| a large phylum of bacteria hat includes many of the common gram-negative bacteria, such as escherichia coli |
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| Protist |
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| algae and protozoa |
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| Resolution |
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| in microbiology, the ability to distinguish two objects as distinct and separate under the microscope |
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| ribosome |
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| a cytoplasmic particle that functions in protein synthesis |
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| Virus |
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| A genetic element that contains either a DNA or an RNA genome, has an extracellular form and depends on a host cell for replication |
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| Allele |
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| A sequence variant of given gene |
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| Banded iron formation |
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| iron oxide-rich ancient sedimentary rocks containing zones of oxidized iron formed by oxidation of Fe2+ by O2 produced by cyanobacteria |
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| Binomial System |
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| the system devised by the Swedish scientist Carl linnaeu for naming living organism in which an organism is given a genus name and a species epithet |
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| Cladistics |
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| Phylogenetic methods that group organisms by their evolutionary relationships,not by their phenotypic similarities |
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| Domain |
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| in a taxonomic sense, the highest level of biological classification |
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| DNA- DNA hybridization |
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| the experimental determination of genomic similarity by measuring the extent of hybridization of DNA from one organism with that of another |
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| ecotype |
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| a population of genetically identical cells sharing a particular resource within an ecological niche |
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| Endosymbiotic hypothesis |
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| the idea that a chemoorganotrophic bacterium and a canobacterium were stably incorporated into another cell type to five rise, respectively, to the mitochondria and chloroplasts of modern day eukaryotes |
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| Eukarya |
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| all eukaryotes: algae, protist, fungi, slime molds, plants and animals |
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| Evolution |
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| decent with modification; DNA sequence variation and the inheritance of that variation |
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| FAME |
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| Fatty acid methyl ester; a technique for identifying microorganisms from their fatty acids |
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| FISH |
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| fluorescent in situ hybridization; a staining technique for phylogenic studies |
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| Fitness |
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| the capacity of an organism to survive and reproduce as compared to that of competing organisms |
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| GC ratio |
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| in DNA form an organism, the percentage of the total nucleic acid that consists of guanine and cytosine bases. |
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| Horizontal gene transfer |
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| the transfer of DNA from one cell to another, possibly distantly related, cell |
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| molecular clock |
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| a DNA sequence such as the gene for rRNA that can be used as a comparative temporal measure of evolutionary divergence |
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| Monophyletic |
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| In phylogeny, a group descended from one ancestor |
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| Multilocus sequence typing (MLST) |
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| a taxonomic tool for classifying organisms from gene sequence variation in several house keeping genes |
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| Phylogenetic probe |
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| an oligonucleotide, sometimes made fluorescent by attachment of a dye, complementary in sequence to some sequence in rRNA |
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| Phylogeny |
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| the evolutionary history of an organism |
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| Ribosomal Database Project (RDP) |
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| a large database of small subunit rRNA sequences that can be retrieved electronically and used in comparative rRNA sequence studies |
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| Ribotyping |
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| a means of identifying microorganisms from analysis of DNA fragments generated from restriction enzyme digestion of the genes encoding their 16S rRNA |
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| 16S rRNA |
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| a large polynucleotide that functions as part of the small subunit of the ribosome of Bacteria and Archaea and form whose gene sequence evolutionary information can be obtained its eukaryotic counterpart is 18S rRNA |
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| Small Subunit rRNA |
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| RNA from the 30S ribosomal subunit of Bacteria and Archaea or the 40S ribosomal subunit of eukaryotes that is, 16S or 18S rRNA, respectively |
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| Species |
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| defined in microbiology as a group of strains that all share the same major properties and differ in one of more significant properties from other groups of strains; defined phylogenetically as a monophyletic exclusive group based on DNA sequence analyses |
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| Stromatolite |
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| a laminated microbial mat, typically built from layers of filamentous Bacteria and other microorganism which can become fossilized |
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| Systematics |
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| The study of the diversity of organisms and their relationships includes taxonomy and phylogeny |
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| Taxonomy |
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| the science of identification, classification and nomenclature |
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| Universal phylogenic tree |
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| a tree that shows the positions of representatives of all domains of cells |
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| proteobacteria |
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| a major lineage of Bacteria that contains a large number of gram-negative rods and cocci |
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| nucleic acid probe |
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| an oligonucleotide, usually 10-20 bases in length, complementary in base sequence to a nucleic acid sequence in a target gene or RNA |
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| Fluorescent in situ hybridization (FISH) |
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| a method employing a fluorescent dye covalently bonded to a specific nucleic acid probe for identifying of tracking organisms in the environment |
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| Anoxic |
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| Oxygen free |
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| Fermentation |
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| Anaerobic catabolism of an organic compound in which the compound serves as both an electron donor and an electron acceptor and in which ATP is usually produced by substrate level phosphorylation |
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| Hydrogenase |
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| An enzyme widely distributed in anaerobic microorganisms, capable od oxidizing of evolving H2 |
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| Homofermentative |
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| Producing only lactic acid from the fermentation of glucose |
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| Heterofermentative |
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| Producing a mixture of products, typically lactate, ethanol,and CO2,from the fermentation of glucose |
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| Stick land reaction |
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| The fermentation of an amino acid pair |
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| Secondary fermentation |
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| A fermentTion in which the substrates are the fermentation products of other organism |
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| Syntrophy |
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| A process whereby two or more microorganisms cooperate to degrade a substrate neither can degrade alone |
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| Free energy G |
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| Energy available to do work,G0 is free energy under standard conditions |
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| Exergonic |
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| Release energy |
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| Activation energy |
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| The energy required to bring the substrate of an enzyme to the reaction state |
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| Catalyst |
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| A substrate that accelerates a chemical reaction but is not consumed in the reaction |
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| Enzyme |
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| A protein that can speed up a specific chemical reaction |
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| Coenzyme |
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| A small and loosely bound nonprotein molecule that participates in a reaction as a part of an enzyme |
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| Electron donor |
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| A substance that can donate electrons to an electron acceptor,becoming oxidized in the process |
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| Electron acceptor |
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| A substance that can accept electrons from an electron donor, becoming reduced in the process |
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| Reduction potential |
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| E0' the inherent tendency, measured in volts under standard conditions, of a compound to donate electrons |
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| Adenosine triphosphate ATP |
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| A nucleotide that is the primary form in which chemical energy is conserved and utilized in cells |
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| Fermentation |
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| Anaerobic catabolism in which an organic compound is both an electron donor and an electron acceptor and ATP is produced by substrate level phosphorlation |
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| Respiration |
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| The process by which a compound is oxidized with O2, as the terminal electron acceptor usually accompanied by ATP production by oxidative phosphorylation |
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| Substrate level phosphorylation |
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| Production of ATP by the direct transfer of an energy rich phosphate molecule from a phosphorylated organic compound to ADP |
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| Glycolysis |
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| A biochemical pathway in which glucose is fermented, yielding ATP and various fermentation products,also called en den Meyer old parkas pathway |
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| Oxidative phosphorylation |
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| The production of ATP from a photon motive force forced by electron transport of electrons from organic or inorganic electron donors |
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| Proton motive force Pmf |
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| A source of energy resulting from the seperation of protons from hydroxyl ions across the cytoplasmic membrane, generating a membrane potential |
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| ATP synthase atpase |
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| A multi protein enzyme complex embedded in the cytoplasmic membrane that catalysts the synthesis of ATP coupled to dissipation of the proton motive force |
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| Citric acid cycle |
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| A cyclical series of reactions resulting in the conversion of acetate to two molecules of CO2 |
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| photosynthesis |
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| a series of reactions in which ATP is synthesized by light-driven reactions and CO2 is fixed into cell material |
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| phototrophs |
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| an organism that uses light as an energy source |
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| autotroph |
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| an organism that uses CO2 as its sole carbon source |
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| oxygenic photosynthesis |
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| photosynthesis carried out by cyanobacteria and green plants in which O2 is evolved |
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| AN-oxygenic photosynthesis |
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| photosynthesis in which O2 is not produced |
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| chlorophyll |
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| a light sensitive Mg containing porphyrin of phototrophic organism that initiates the process of photophosphorylation |
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| bacteriochlorophyll |
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| the chlorophyll pigment of anoxygenic phototrophs |
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| thylakoids |
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| membrane stacks in cyanobacteria or in the chloroplast of eukaryotic phototrophs |
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| antenna pigments |
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| light harvesting cholorophylls or bacteriochlorophylls in photocomplexes that funnel energy to the reaction center |
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| Chlorosome |
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| a cigar-shaped structure present in the periphery of cells of green sulfur and green nonsulfer bacteria and containing the antenna bacteriochlorophylls |
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| carotenoid |
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| a hydrophobic accessory pigment present along with chlorophyll in photosynthetic membranes |
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| phycobiliprotein |
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| the antenna pigment complex in cyanobacteria that contains phycocyanin and allophycocyanin or phycoerythrin coupled to proteins |
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| phycobilisome |
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| an aggregate of phycobiliproteins |
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| photophosphorylation |
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| the production ATP in photosynthesis |
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| reverse electron transport |
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| the energy dependent movement of electrons against the thermodynamic gradient to form a strong thermodynamic gradient to form a strong reductant from a weaker electron donor |
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| chemolithotroph |
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| a microorganism that oxidizes inorganic compounds as electron donors in energy metabolism |
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| mixotrophs |
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| an organism in which an inorganic compound serves as the electron donor in energy metabolism and organic compounds serve as the carbon source |
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| hydrogenase |
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| an enzyme, widely distributed in anaerobic microorganisms, capable of taking up or evolving H2 |
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| nitrification |
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| the microbial conversion of NH3 to NO3- |
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| anammox |
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| anoxic ammonia oxdation |
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| crearchaeota |
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| a phylum of archaea that contains both hyperthermophilic and colddwelling organisms |
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| hyperthermophiles |
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| an organism with a growth temperature optimum of 80 degrees Celsius or greater |
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| extreme halophile |
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| an organism whose growth is dependent on large concentrations (generally 9% or more) of NaCl |
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| compatible solute |
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| an organic or inorganic substance accumulated in the cytoplasm of a halophilic organism that maintains osmotic pressure |
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| halorhodopsin |
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| a light driven chloride pump that accumulates Cl- within the cytoplasm |
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| methanogens |
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| a CH4- producing organism |
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| solfatara |
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| a hot, sulfur rich generally acidic environment commonly inhabited by hyperthermophilic archaea |
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| hydrothermal vents |
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| a deep sea hot spring emitting warm (~20 degrees C) to superheated (>300 degrees C) water |
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| thermosome |
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| a heat shock (chaperonin) protein complex that functions to refold partially heat denatured proteins in hyperthermophiles |
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| reverse DNA gyrase |
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| a protein universally present in hyperthermophiles that introduces positive supercoils into circular DNA |
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| banded iron formations |
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| iron oxide-rich ancient sedimentary rocks containing zones of oxidized iron (Fe3+) formed by oxidation of Fe2+ by O2 produced by cyanobacteria |
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| thalassemia |
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| a genetic trait that confers resistance to malaria, but causes a reduction in the efficiency of red blood cells by altering a red blood cell enzyme |
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| Sickle cell trait |
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| a genetic trait that confers resistance to malaria, but causes a reduction in the oxygen-carrying capacity of the blood by reducing the life expectancy of the affected read blood cells |
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| Malaria |
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| a disease characterized by recurrent episodes of fever and anemia, caused by the protist Plasmodium spp. usually transmitted between mammals through the bite of the anopheles mosquito |
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| eukaryotes |
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| a cell or organism having a unit membrane-enclosed nucleus and usually other organelles; a member of eukarya |
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| histones |
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| a positively charged proteins that package eukaryotic DNA in nucleosomes |
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| cristae |
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| the internal membranes of a mitrocondrion |
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| hydrogenosome |
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| a organelle of endosymbiotic origin present in certain anaerobic eukaryotic microorganisms that functions to oxidize pyruvate to H2, CO2 and acetate along with the production of one molecule of ATP |
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| chloroplast |
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| the photosynthetic organelle of eukaryotic phototrophs |
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| calvin cycle |
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| the series of biosynthetic reactions by which most photosynthetic organisms convert CO2 to organic compounds |
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| Endosymbiotic hypothesis |
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| the idea that a chemoorganotrophic bacterium and a cyanobacterium were stably incorporated into another cell type to give rise, respectively, to the mitochondria and chloroplasts of modern-day eukaryotes |
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| cytoskeleton |
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| the cellular scaffolding typical of eukaryotic cells in which microtubules microfilaments, and intermediate filaments define the cell's shape |
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| Extracellular matrix |
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| ECM - Proteins and polysaccharides that surround an animal cell and in which the cell is embedded |
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| Eukarya |
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| eukaryotic organisms |
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| ciliates |
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| any protist characterized in part by rapid motility driven by numerous short appendages called cilia |
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| Fungi |
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| nonphototrophic eukaryotic microorganisms with rigid cell walls |
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| Conidia |
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| the asexual spores of fungi |
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| chitin |
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| a polymer of N-acetylglucosamine commonly found in the cel walls of fungi |
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| algae |
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| phototrophic eukaryotes, both microorganism and macro-organisms |
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| colonial |
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| the growth form of certain protists and green algae in which several cells live together and cooperate for feeding; motility of reproduction; an early form of multcellularity |
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| nucleus |
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| the organelle that contains the eukaryotic cells chromosomes |
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| mitrochondrion |
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| the respiratory organelle of eukaryotic organisms |
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| stroma |
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| the lumen of the chloroplast, surrounded by the inner membrane |
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| thylakoids |
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| a membrane layer containing the photosynthetic pigments in chloroplasts |
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| lysosomes |
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| an organelle containing digestive enzymes for hydrolysis of proteins, fats and polysaccharides |
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| peroxisome |
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| an organelle that functions to rid the cell of toxic substances such as peroxides, alcohols, and fatty acids |
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| microtubules |
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| a filamentous polymer of the protein alfa tubulin and beta tubulin that functions in eukaryotic call shape and motility |
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| microfilaments |
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| a filamentous polymer of the protein actin that helps maintain the shape of a eukaryotic cell |
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| intermediate filament |
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| a filamentous polymer of fibrous keratin proteins, supercoiled into thicker fibers, that functions in maintaining cell shape an the positioning of certain organelles in the eukaryotic cell |
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| Protist |
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| a unicellular eukaryotic microorganism may be flagellate or aflagellate, phototrophic or nonphototrophic and most lack cell walls includes algae and protazoa |
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| phagocytosis |
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| a mechanism for ingesting particulate material in which a portion of the cytoplasmic membrane surrounds the particle and brings it into the cell |
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| Slime Mold |
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| a nonphototrophic protist that lacks cell walls and that aggregates to form fruiting structure or masses of protoplasm |
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| mushrooms |
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| the aboveground fruiting body, or basidiocarp, of basidiomycete fungi |
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| yeasts |
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| the single-celled growth form of various fungi |
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| FtsZ |
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| a protein that forms a ring along the midcell division plane to initiate cell division |
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| Divisome |
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| a complex of proteins that directs cell division process in prokaryotes |
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| transpeptidation |
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| formation of peptide crossing links between muramic acid residues in peptidoglycan synthesis |
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| Cytoplasmic membrane |
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| the permeability barrier of the cell, separating the cytoplasm from the environment |
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| simple transport system |
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| a transporter that consists of only a membrane spanning protein and is typically driven by energy from the proton motive force |
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| ABC transport |
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| a membrane transport system consisting of three proteins, one of which hydrolyzes ATP, the system transports specific nutrients into the cell |
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| gram positive |
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| a bacterial cell whose cell wall consists chiefly of peptidoglycan; it lacks the outer membrane of gram negative cells |
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| gram negative |
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| a bacterial cell with a cell wall containing small amounts of peptidoglycan and an outer membrane containing lipopolysaccharide, lipoprotein, and other complex macromolecules |
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| gram stain |
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| a differential staining procedure that stains cells either purple (+) or pink (-) |
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| peptidoglycan |
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| a polysaccharide composed of alternating repeats of N-acetylmuramic acid arranged in adjacent layers and cross-linked by short peptides |
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| teichoic acid |
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| a phosphorylated polyalcohol found in the cell wall of some gram-positive bacteria |
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| outer membrane |
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| a phospholipid and polysaccharide- containing unit membrane that lies external to the peptidoglycan layer in cells of gram negative bacteria |
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| periplasm |
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| a gel like region between the outer surface of the cytoplasmic membrane and the inner surface of the lipopolysaccharide layer of gram negative bacteria |
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| S layer |
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| an outermost cell surface layer composed of protein or glycoprotein present on some bacteria and archaea |
